Sleeper Agent
by PrincessEspie
Summary: Lazarus was more than just a project. She's come for the first time, with a vengeance. How many times can a certain Commander escape Death before he decides to come and collect? Will her crew be able to save her before Lazarus takes her for good?


_**Sleeper Agent**_

**My Comments :**

One of the stories I have going is a (surprise surprise) story about Mass Effect. Because of how long it is, thoughts of how to end it have been running rampant around my brain. Since the dreams are just becoming obnoxious, I've decided to write it down. The only reason I'm posting this is that I decided this wouldn't be the ending to my other story.

However, some things said might refer to my other story, so I'll tell you a little bit about what would have happened so far. This way, you are not obligated to read the other one. _"Sleeper Agent"_ takes place after Mass Effect 3, after Shepard choose the 'Control' option. Three years later, Monarch and the other Reapers rebuild Shepard and allow her to join the crew again. Most of the old crew is there, including her boyfriend, Garrus Vakarian. This particular story takes place before any of the characters I created (other than Monarch) were introduced.

I hope you enjoy!

**The Story :**

Shepard could remember that day clearly. Waking up, seeing the Reaper AI and thinking, _'oh. That's Monarch.'_ She could tell the Reapers' names just by looking at them. Not only that, but she knew that she had them completely under her control. Even then, they didn't do much in the fixing of her body when they brought her back. They, being the Reapers, could have easily removed the implants her scientist mother had put in her non-biotic daughter as a young child. Or gotten rid of that damn scar Garrus had left on her back before the final battle.

The Commander sighed, falling back on her bed. Her long red raid spread out along the bed, reminding her that since she was Alliance again, she'd probably have to cut it. On the other end of the room, Cinders squeaked again, telling her owner she needed to be fed. Shepard vaguely made a note to herself to get an automatic feeder for the hamster too.

"_Commander?"_ Joker's tired voice filtered in from the Comm, _"we've arrived at the Citadel."_

Shepard sighed inaudibly. She could deal with all that bureaucratic crap in the morning. "Thanks, Joker. Get some sleep in a real bed tonight, alright?"

"_Is that an order?"_

"You bet, Moreau." She sat up, stretching her arms. Honestly, things weren't that bad. Shepard was glad to be back at all. Besides, the implants her damn Cerberus stooge of a mother had put in would have killed her a year or two after the end of the war regardless. Now, the Reapers had managed to add quite a few years to that total. Maybe her mother wasn't so bad in the long run. Without her screwing up the Commander's childhood, she'd never have had Anderson as a father, the strength she now possessed, and she definitely wouldn't have met Garrus. But still, that damn woman was the reason Mindoir was attacked and her best friend Leo was killed. At least the bitch died during the attack. And she got adopted by Anderson after, so it all worked out.

Shepard stood, preparing to get into some pajamas when her Omni-Tool beeped. "What's this?" She clicked the button, revealing a blank screen with audio.

"_The loss of many can affect the greater good. Activate, sleeper agent Lazarus."_

~ Break ~

That is when everything went black.

"Doctor T'soni?"

Liara groaned loudly into her pillow, grimacing. She put both arms on either side of the pillow, pushing herself up. "What is it, Glyph? You're programmed to let me sleep, aren't you?"

The machine nodded. "This is a priority one alert."

The Shadow Broker jumped straight of bed, disregarding the fact she was barely wearing anything. "What happened, Glyph?" She ran to her terminals.

"Cerberus sleeper agent 001 has been activated."

"What's their name?"

"That data is still unknown."

"Damn it all," the Asari muttered under her breath. "Call down Miranda and ask EDI to help decode that file."

"Yes, doctor."

Liara continued to type away at her keyboard until a very disgusted sounding Miranda came in.

"What is it, Liara? Everyone on the ship is sleeping."

The Shadow Broker bit her lip. "Do you know anything about 001?"

"The sleeper agents again? I already told you, Liara. The sleeper agent project was scrapped for years. It was revitalized when I came back. I only programmed agents 002 through 342. And all of those are either incapacitated or dead. I made sure of that by myself." Miranda leaned against the door frame, smoothing out her skin-tight suit. "Is there a specific reason for bringing this up again? If you've forgotten, I don't work with Cerberus anymore."

"001 was activated," Liara said, frowning. "Just now."

"Have you found out who it is?" Miranda immediately questioned, joining the Asari at the terminal.

"Not ye-"

"Liara T'Soni," EDI's platform joined the duo, watching both jump in surprise. "We must leave."

"Excuse me?" Liara growled, narrowing her eyes.

"Sleeper agent 001 has been identified. She is on the Citadel, with access to anywhere she desires."

"What are you talking about?" Miranda snapped back, her eyes vicious.

EDI's expression didn't change. "Garrus Vakarian and Kaidan Alenko are getting into their armor and preparing their weapons. The Councilors have already agreed to their boarding the Citadel with their weapons."

"Who _is_ it?" Liara snarled.

"Agent 001 is Commander Shepard. Project Lazarus."

~ Break ~

Lazarus fixed the cloak on her shoulders, making sure it covered her face. Her golden eyes darted around the docking bay, a light scowl on her face. There were too many people. How was she supposed to blend in? She grit her teeth, walking through the security checkpoint. The officer looked surprised, but a glare cut off anything he had thought about saying. Without a sound she pressed a button on the elevator, prepared to began her mission.

As the door opened to the Presidium Commons, Lazarus wasted no time in stepping out, heading to her destination. Her agent on the inside. She was well aware that no other sleeper agents got this kind of care. According to what little information she had, she was special. Still, her mission was one of high importance. Should her mission fail, the fate of Cerberus would be at stake. The fate of Cerberus was of the utmost importance right now. It was the reason she existed.

As Kannik came into view, her expression went completely neutral. No need for that damned Salarian to know what she was feeling. It was bad enough that an alien was a member of Cerberus. Of course, he was only a part of the _extremely _small Citadel cell. There were probably one or two more people she could have gone to in order to get her weapons for the assassination, but they were all aliens. Not even deserving of the term 'people'. Besides, it was easiest to get to Kannik. And he was always in the same area. Made it easier to kill him if she had to later.

"Hello?" The Salarian began, confused. "What can I help you with?"

"Kannik," Lazarus began, her voice slightly lower than anyone would remember. "I am agent 001."

Kannik's eyes widened. "L-Lazarus?!" he exclaimed in a hushed voice. "Please. Come this way." He led her to the back room. "I thought the sleeper agents were scrapped!"

"I am not forced to answer your questions, alien. I am merely here to recover my weaponry." Lazarus studied him with her bright golden eyes that were shining beneath the cloak.

"And why should I?"

"Because I have other sources and could easily kill you now," she responded, not missing a beat. "It is imperative I retrieve my weapon _now_."

Kannik sighed, digging through the boxes until he found two. "Here," the Salarian grumbled. He opened the larger one, revealing a Widow sniper rifle. "It can be compacted into an extremely small size," he explained, holding it out.

Lazarus checked it, nodding with approval as she pressed a small button. It slowly folded into itself before becoming the size of a thick datapad. "It shall work," she stated.

He growled under his breath, glaring at her. "Ungrateful little," he mumbled before opening the other box. "A form of the Paladin," he explained. "Unable to detect by the scanners. Should be useful if you run into problems."

Lazarus grabbed the gun, lifting her cloak for just a moment before clipping it to her belt. "These shall do," she said, turning. "I appreciate the help, alien. Perhaps Cerberus will let you die quickly instead of becoming a slave."

~ Break ~

Garrus grimaced as Kaidan yawned for the third time. His bright blue eyes tiredly surveyed their surroundings. The CIC was completely empty, everyone was sleeping. They were docked on the Citadel, so there wasn't any need for night shifts. Besides, Shepard was off doing something on the station, so the crew would have a warning before she even got here. In the cockpit, Joker was snoring, likely disobeying a direct order from his fiance again. What was confusing in all of this was the fact that EDI had chosen to wake only the two of them up, telling them Liara would meet them up here. Plus, she had told them to get in their armor and grab their weapons. They weren't even allowed to bring weaponry on the Citadel!

Kaidan yawned again. "What do you think this is all about? Think the Commander ran into some trouble?"

Garrus shook his head to clear away his prior thoughts. "Not at all. If she were in trouble, EDI would wake up the whole damn ship. And if she wanted us for something, Shepard would have called us and woken us up herself."

"Yeah," Kaidan agreed, frowning. "EDI sounded kind of nervous though. I've never heard her like that before."

The Turian nodded. "She wasn't even like that while the rest of us attacked the Collector base."

The second Human Spectre visibly flinched, his mouth forming a thin line. He scratched the back of his neck, cheeks a light pink. Garrus had learned enough about Human emotions to know he was embarrassed and a little angry with himself. That damned guy should be. Garrus remembered how torn up Shepard had been, as if her heart had been ripped apart. He recalled asking Karin if someone could die from the emotional trauma, worried about how Shepard had so easily faked bouncing back. The worry had worsened when the doctor had informed him that Humans have 'heart strings' that can actually break if the emotional trauma is great enough, killing the person. Still, Shepard had seemed physically fine so he his only concern had been about how long she could last like that.

Kaidan was remembering how distant she had been when she met him again. He knew she only spoke to him because she had to, causing Vega to become slightly protective of her. And once Vega knew the real reason, he become three times as protective. When he returned to the ship, the soldier would do everything he could to lead Shepard away from him or distract him long enough for the Commander to get by. Even then, Shepard would sometimes bring him on missions. Never with Garrus, he had vaguely noted, though at the time he didn't know why. Usually Javik or Vega. Now he knew why. Both did an really good job of keeping him as far away from her as possible. And when he had finally asked to meet her, she said they were over, no hesitation. Though he'd admit she did say it nicely.

The sound of the elevator doors opening caused both to shake their heads to clear their thoughts. Liara, Miranda, and EDI ran out, all three dressed in armor and carrying their usual weaponry. The Shadow Broker wasted no time in typing in the code to open the doors as EDI woke up a very annoyed Joker.

"What's going on, Liara?" Kaidan finally asked.

The doors opened and they all stepped in, EDI joining them a few moments later. Once the doors closed, Liara ignored them completely, opting to type furiously away at her Omni-Tool instead. EDI was staring blankly at a wall, probably going through some sort of calculations. Miranda was just fidgeting.

"What is going on?" Kaidan repeated, clenching his fists.

Garrus noted that, other than EDI who didn't have one, everyone's pulse was elevated.

Liara glanced up. "Miranda? I'm checking Citadel security for her location. Can you explain?" She looked back down.

Miranda nodded. "Cerberus had a special program." She glared at the duo's eyes rolls. "One of many, I realize, but this one was one of the most important. It was a project tailored to the design of sleeper agents. I programmed numbers 002 through 342. All of which had been taken care of. According to Liara, 001 has been activated."

"001? Why weren't they taken care of too?"

Miranda narrowed her eyes at Garrus. "_Because_ I wasn't the one to program them. No one, barring the Illusive Man, knew who she was."

"She?" Kaidan questioned, raising an eyebrow.

EDI glanced over. "Sleeper agent 001 goes by the name Lazarus," she said calmly.

Garrus' heart stopped beating for a few moments, his lungs freezing up as well. It couldn't be. "L-Lazarus?" he finally made out as his organs started working again. "You mean _Shepard_ is the first sleeper agent?!"

Kaidan's heart skipped a beat. "You mean that's why we brought our guns? Because of _Shepard_?!"

Miranda stamped her foot, practically snarling her next words, "that _thing_ out there is _not Shepard!_ Whatever is out there is a mindless body created by Cerberus to do their damn dirty work! That agent may _look_ like Shepard, but on the inside, she is Lazarus. A cold, emotionless killer with one job to do! To make Cerberus rise to the top!" Miranda clenched her fists, looking away. "Damn it! If only I had done more research! If I could have just figured out who it was!" One of her arms raised and she smacked the door back into the ship. "If I could have just done something," she muttered, staring at the ground as her arm fell limply to her side.

_His name was Garrus Vakarian, and if he had a say in it, he'd save the woman he loved._

The outer doors opened, revealing a nervously pacing Bailey. He seemed to sigh with relief when he spotted them.

Liara barely noticed him, walking straight out the door. She paused before jumping up. "I've got her!" she exclaimed, relief evident in her voice. "She left the Normandy about thirty minutes ago and passed through the checkpoint going to the elevator."

Bailey's face paled. "What _exactly_ is going on? Is Shepard really a sleeper agent?"

The Shadow Broker waved her free arm dismissively. "Yes. Right now we need to track her. It's hard because she's wearing a cloak and keeps activating her tactical cloak." Her hand moved masterfully over the controls. "Here! She went in to see Kannik!"

"Kannik?" Garrus questioned, his eyes narrowing. "You mean that guy we had to bribe to get C-Sec those weapons?"

Bailey narrowed his eyes. "Excuse me?"

"Not important," Liara said, continuing to type away. "After that she went back to the elevator. She got out at the Embassies."

Miranda visibly paled to the point she was almost pure white. "The _Embassies?!_"

"Yes," Liara confirmed, looking up. "Is something wrong?"

"There's a reason sleeper agents are what they are!" Miranda began pacing. "They are generally sent to make Cerberus more powerful. Do you know what that means?!" She glanced to see the confused stares. "She's going to kill someone! Why else would she go to Kannik? The guy sells weapons!"

No one moved. No one said a word. And no one knew what to do next.

~ Break ~

Lazarus moved through the Embassies with purpose. It was one of the many rules when you're doing something you're not supposed to be; look like you belong. As far anyone else knew, she _did_ belong. This was where she needed to be right now. Performing an assassination. Under the cloak her eyes looked directly ahead. Averting her eyes would look suspicious. The only time is was necessary to move her eyes was to nod to the C-Sec officer stationed outside of the Spectre offices. Idiot was none the wiser. Though, she should be happy the guy was an idiot; meant he was easier to control. There was the fact that she was a Spectre, of course. That in itself granted her the ability to not get second looks. Which in her current assignment, was pretty damn helpful.

Her eyes darted around the offices. Perfect. As usual, no one was here. No time to waste. Lazarus went to the far wall, prying the nearly invisible grate off of it. She smirked. The blueprints were absolutely perfect. She jumped in, replacing the grate once she was securely inside. As much as she _loved_ crawling through ducts, the faster she went the better. Besides, there was no telling how long her target would be in their office. Sure it would be easy enough to track them, but the best way to achieve her goal would be to kill them in their office. And the longer she waited in the ducts, the higher the risk of her being caught.

A light caught her eye. Lazarus inched forward a few feet, looking down. The hallway. The route was easy from here. She continued on. Then all she had to do was take out the grate, shoot them with the silenced rifle, replace the grate, and shuffle back to the Spectre offices like nothing happened. Of course, nothing ever goes exactly as planned. So if she can't reach the target with the rifle, it would be just as easy with the hand gun. As she neared her target, she heard voices through the grate. Now it was time to play the waiting game. Once the possible bystander was gone, all she had to do was remove the grate and shoot the target.

And just like that. He would be dead.

~ Break ~

The silence continued in the elevator, and it was by _no_ means comfortable. The only sounds heard was the Liara's typing and the grating of cable and pulley as the elevator moved to its destination. Kaidan's feet were silent as he shifted back and force, his heart rate getting so high he would probably go into cardiac arrest soon. Bailey was in the back, one of his eyes twitching ever so slightly. Miranda's fists were still clenched, her eyes locked on the corner as if something there were particularly interesting. EDI's expression was as blank as ever.

And then there was Garrus. Unlike the others, his mind wasn't even on the situation at hand. In all honesty, he had told himself he would snap back to reality once the doors opened and they checked the newest footage to figure out where she'd gone. For now though, the Turian could only think about the woman he loved with all of his heart. Who she had been and what she had done. Not just for the galaxy, but for him. If he hadn't met Shepard all those years ago, there was no doubt in his mind that he wouldn't be who he was today. Before, he never really had a purpose. He was just trying to be like his dad and become the best damn C-Sec officer possible. Now, he knew that Shepard had showed him that sometimes, if you yell loud enough, someone will come over to see what all the fuss is about. And sometimes, that is just what needs to happen.

"Let's go," Liara called out, running towards the offices. "According to what I have, Shepard was last seen going into the Spectre offices." She slid to a stop outside, frowning at the door.

"Council didn't give you permission to go in there," Bailey reminded them. "If this wasn't such a time sensitive mission they wouldn't have allowed you on the station at all."

Kaidan stepped forward, waving his Omni-Tool in front of the door. "Come on. The terminals will be locked down, but I can get you in."

Liara shook her head. "You stay out here and communicate with me through comms. Don't worry. From in there I can feed you all the information you need." She ran through, the doors closing shut behind her. _"Can everyone hear me?"_

"Loud and clear, Liara. Did Shep leave a trace?"

"_Not that I can tell yet, Garrus. She seems to have- Oh!"_ The comms were filled with a loud grunt and a crash. _"Shepard went through the ducts. I'm checking the motion scanners for where she went."_ Silence filled the line.

"Liara?" Miranda questioned, a scowl lining her perfect features. "Mind telling us what you found?"

"_Still checking,"_ came the quiet response. _"By the Goddess! Shepard's going after Hackett!"_

The group spun a half circle as the door opened. A young human froze when he saw them before running away in fear. Hackett was facing the windows. On the ceiling, a grate was being lifted. The door began to shut as a figure draped in black dropped from the grate.

"Shepard!" Garrus lunged towards the door, causing it to stop closing and open again. The rest of the group followed him in, drawing their weapons. Hacket spun in confusion, surprise covering his face when he realized who was pointing a gun at him.

_His name was Garrus Vakarian, and he'd protect Shepard with his life if he had to._

Keeping her gun steady, the cloaked figure turned her head towards the newcomers. "My name is not Shepard," she said calmly, "my name is Lazarus."

Miranda groaned. "She's too far gone. We need to deactivate Lazarus to get Shepard back." Her grip on her gun tightened.

Kaidan tried to speak calmly, but his voice cracked anyway, "we need you to back down. Now."

"Why should I? I can still complete my mission." Lazarus turned back to Hackett. "And in order for Cerberus to become as powerful as it needs to be, you must be destroyed."

As her finger began to tighten, a green figured clothed in black jumped down from the vents, hitting a pressure point on the woman's shoulder with one smooth move. He caught her as she fell into his arms, her gun clattering to the floor.

"Kolyat?" Garrus questioned, his mandibles flaring in surprise.

"I heard of her situation," he said vaguely, bringing her to Garrus. "I was only to step in if it was unavoidable."

"Who told you?" Kaidan snapped.

"_That would be me_," Joker said into the comms with as much happiness to ease the mood as he could muster. _"The whole damn crew's awake. And if they don't get the order to head over to wherever you're bring the Commander soon, they'll just break out."_

"And would they do that?" Bailey growled.

"_We have two Krogans on board."_

~ Break ~

Liara eyed the panel with a frown, ignoring Garrus muttering to himself next to her. So far, none of the brain scans had shown anything remotely helpful. It seems the only areas of activity were her implants that her mother, Espie Shepard, had put in. Whatever was in those implants was causing Lazarus to become active. Unfortunately, no one knew how to take them out without killing the host, Shepard. Speaking of the Commander, she was just barely waking up inside of the room.

Shepard and the chair she was strapped to were the only things in the room besides the light above her head. Her legs and lower arms were strapped to the chair, greatly restricting her movements. Medication that coursed through her veins dulled her biotics to a point where they were completely useless. As her eyelids stopped fluttering and she began to fully grasp the situation, she began to struggle.

"Any luck?" Miranda asked, returning with a cup of coffee.

"No, but she's waking up," Liara informed her.

"Has she stood up yet and started walking around?"

"No. Why would she? She's strapped to the chair."

The cup of coffee smashed to the ground and Miranda paled. "You did _what?!_ Do you know what sleeper agents are programmed to do when they are trapped with no chance of escape?"

Garrus inched closer to the door, mandibles pressed tightly to his face in worry. "No. What?"

"They're programmed to end their lives to their information doesn't leak out!"

The Turian's eyes narrowed as he glanced at the camera. Sure enough, Lazarus had realized her current situation and had began to claw at her own wrists. When they became raw, Garrus had apparently had enough and burst through the door, undoing the bindings.

"Hm?" Lazarus hummed in confusion, back flipping over the chair to get some distance between her and the Turian. "How dare you touch me," she snarled.

Garrus had absolutely nothing to say. The person before him was physically Shepard, and she never had so much contempt in her eyes before. Not at him anyway. He left the room, moping near the screens. Immediately, he could see Lazarus run to the opposite corner, checking for an escape opportunity.

Liara shook her head. "We need to talk to her. Try to distract her for as long as possible so I can work on how to get those implants out without killing her."

Miranda nodded. "I'm on it." She stepped carefully through the door, noting how the agent fell into line immediately when she stepped through. "My name is Miranda Lawson. I work for Cerberus. Give me your information."

Lazarus saluted her before standing at attention. "Sleeper Agent 001. Lazarus."

"Mission?"

"To better the human race by helping Cerberus."

"Specific mission," she specified with a growl.

Lazarus nodded. "To set the other species against each other."

"And how would this be achieved?"

"By killing humanity's voice on the Citadel, the humans would grow to suspect the aliens responsible. Due to the place of the assassination, the aliens would suspect the other species had done it. With other small adjustments, this would soon lead to a war. When the other species had worn themselves out, humanity could claim what is rightfully theirs."

"Right," Miranda said with a nod, playing her part beautifully. "You said adjustments. Sleeper agents are given very specific instructions."

"I was programmed with the ability to alter the plan slightly to increase its efficiency. My unit was the only unit designated with this ability due to the nature of my mission."

Biting her lip, Miranda realized that this meant taking the implants out was going to be even harder. They were self improving. "That'll be all, 001." She turned to leave, hearing the door hiss open. Before she could even step through, he face smashed against the ground and Garrus' voice ran clear;

"Get Shepard!"

~ Break ~

The entire crew, plus Kolyat, had joined the chase for Lazarus. Regardless, she was too fast and agile to catch up to. As long as she had land ahead of her, she would find a path that kept her safe from capture. Unfortunately, this is also how they ended up in a large platform with no railings over looking the Presidium. The place was under construction, and she'd managed to use the equipment to her advantage until now. Now there was nowhere to go and no more equipment to use. The whole crew was surrounding her. But now, she was somewhere Shepard and Garrus knew well. It was his favorite place on the Citadel.

"Give up!" someone yelled.

"Just stop running!" yelled another.

Lazarus spun to face them, her face emotionless. She threw off her cloak, allowing it to drift away. "It appears this escape attempt was not successful," she said with a frown, tapping her chin thoughtfully. "Perhaps the smartest option would be to return to custody."

Many of them seemed relieved, but kept their weapons raised. Garrus was the one to move forward, one talon hovering over his gun while the other held a simple pair of cuffs. He approached her slowly, and seeing no attempt at revolt, removed the hand hovering over his gun to bind her hands together. In one swift movement, the Turian suddenly realized Lazarus was behind him slightly, holding his arms behind his back with one hand and holding his gun to his head with the other. The cuffs lay on the ground at their feet. Everyone was tense.

"My mission must be completed," she stated. "No matter what happens. The mission is the only concern." Her eyes narrowed.

Kaidan stepped forward, his anger getting the better of him. "Why can't you just come to terms with the fact that we won't let you complete your mission?!"

Lazarus' muscles tensed. "I," she paused, frowning, "failed?" She smiled, lightly laughing. "I guess I have. I failed!" Her smile immediately faded. "I'm sorry I failed you," she said quietly, slowly lowering the hand holding the gun and taking a small step back, her heels hanging over the edge.

Miranda froze, her eyes widening. "No! She's killing herself!"

Garrus' own eyes widened as he spun, reaching out to grab the woman he loved. His talons barely caught the edge of her sweatshirt, ripping the fabric open. The Turian fell to his knees, reaching over the edge for her as she plummeted towards the ground. He didn't even hear the rest of the crew scream and run for the edge, wanting to be able to save her in any way possible. Her body splashed into the water below. Within a few seconds, a red tint spread into the water. Dead on impact they'd tell him. She had no chance.

_He was Garrus Vakarian, and this place they were never supposed to be was no longer his favorite place on the Citadel._


End file.
